Ben van Beurden, CEO of Royal Dutch Shell, at the annual shareholders' meeting in The Hague. Photograph: Bas Czerwinski/EPA

Ben van Beurden, the new head of Shell, faced a packed room of global investors on Tuesday at the oil group's annual shareholder meeting. In post since March, the 56-year-old Dutchman can expect probing questions about cash flows, capital efficiency, investment projections and so forth.

The list is unsurprising; with investors, it all comes down to the money. How is their capital being spent, what returns is it making and when can they expect to see the profits? It's curious, therefore, that it took a charity, rather than an investor, to inquire about Shell's role in a $1.1bn corruption scandal in Nigeria.

"Investors need to know what's at stake," says Brendan O'Donnell, oil campaigner at the UK-based non-profit Global Witness, which tabled a query at the annual meeting in The Hague. "Shadowy deals are not just bad for people in developing countries, they're bad business."

The case in question refers to a licencing payment that the Nigerian subsidiaries of Shell and Italy's ENI made in 2011 to develop a lucrative, offshore oil block. The money allegedly ended up in the bank account of a private firm, Malabu Oil and Gas, owned by Nigeria's former oil minister, Dan Etete, now under criminal investigation for his involvement in the affair.

Shell has sought to distance itself from the scandal. The British-Dutch company says it paid the Nigerian government, not Malabu, and that it acted lawfully "at all times". Exactly how much Shell and ENI knew about the final destination of their payment remains unclear, however. Global Witness cites court evidence which suggests that Shell negotiated directly with Etete. The company denies the claim.

Regardless of who paid what to whom, there is one clear loser in the whole affair: the Nigerian public. After nearly six decades of oil exploration, the West African petrodollar state has become a watchword for corruption and missed developmental opportunities. The recent abduction of more than 200 schoolgirls by terrorist militia demonstrates the lawless, fragile existence that faces many everyday Nigerians.

Alice Powell, communications coordinator for Publish What You Pay, a coalition of non-profit groups, says: "Had the payment been disclosed, Nigerian civil society could have asked questions about how the money was spent and where it ended up. Instead, citizens lost out on just over $1bn that could have gone on health or education."

International policymakers will be paying close attention to the case as well. Last year, the European Commission passed a directive requiring listed companies to disclose project-level payments, such as those made by Shell and ENI for Oil Block OPL 245 in Nigeria.

The measure reflects similar legislation in Canada and the US - although companies such as Exxon, Chevron and Shell have successfully appealed against the legality of the latter. In a lawsuit presented by the American Petroleum Institute, the oil majors argue that it would harm their competitive advantage (as state-owned oil companies are exempt).

Similarly, Big Oil objects to the new European Union disclosure rules on the grounds that certain governments contractually block them from disclosing project payments. The list includes the likes of China and Qatar. "Companies will effectively be obliged to choose whether to break the law in the EU [European Union] or to break it somewhere else," a Shell spokesperson claims.

At present, Shell is among those pushing to prevent the Securities and Exchange Commission from reintroducing tough disclosure requirements – a step that Global Witness interprets as "lobbying to weaken laws" on transparency. Again, it's an accusation that the oil major rejects. Instead, it points to the fact that it voluntarily discloses its total payments (pdf) to national governments in 14 key markets. The figures include a $4bn tax and royalties' bill in Nigeria in 2013.

So, coming back to the investors in the room, why should they insist that Shell goes further and reveal project-level data? The answer comes back to money. "For investors, project-level information can help them better gauge risk and avoid nasty surprises down the line", says Powell at the Publish What You Pay coalition. A costly case in point is the recent call by Nigeria's House of Representatives to cancel Shell and ENI's exploration contract.

Not all investors are deaf to demands for greater revenue transparency. In a recent letter to the SEC, a group of financial institutions representing $2.85tn in assets under management said project-level disclosure was in keeping with "changing dynamics" in the oil sector – by which they meant the diminishing opportunities for exploration and the consequent need to search for oil in ever more "challenging governance and business environments".

Despite the huge sums at stake, it remains rare for shareholders to request revenue data on a project-by-project basis, says Giuseppe van der Helm, executive director of the Dutch Investors Association for Sustainable Development. "But if investors want to follow the money, the financial streams, then it's important to get a grip on how payments are made at an individual project level."

• This article was amended in 20 May 2014 to change the value of assets under management to $2.85tn not $2.85bn.

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